Jeffrey E. Barrick - Publications

Affiliations: 
Chemistry & Biochemistry University of Texas at Austin, Austin, Texas, U.S.A. 
Area:
effects of mutations on cell physiology
Website:
http://www.cm.utexas.edu/jeffrey_barrick

68 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Zhang X, Deatherage DE, Zheng H, Georgoulis SJ, Barrick JE. Evolution of satellite plasmids can prolong the maintenance of newly acquired accessory genes in bacteria. Nature Communications. 10: 5809. PMID 31863068 DOI: 10.1038/s41467-019-13709-x  0.72
2018 Deatherage DE, Leon D, Rodriguez ÁE, Omar SK, Barrick JE. Directed evolution of Escherichia coli with lower-than-natural plasmid mutation rates. Nucleic Acids Research. PMID 30137492 DOI: 10.1093/nar/gky751  0.72
2017 Good BH, McDonald MJ, Barrick JE, Lenski RE, Desai MM. The dynamics of molecular evolution over 60,000 generations. Nature. PMID 29045390 DOI: 10.1038/nature24287  1
2017 Caglar MU, Houser JR, Barnhart CS, Boutz DR, Carroll SM, Dasgupta A, Lenoir WF, Smith BL, Sridhara V, Sydykova DK, Vander Wood D, Marx CJ, Marcotte EM, Barrick JE, Wilke CO. The E. coli molecular phenotype under different growth conditions. Scientific Reports. 7: 45303. PMID 28417974 DOI: 10.1038/srep45303  0.56
2017 Brown CW, Sridhara V, Boutz DR, Person MD, Marcotte EM, Barrick JE, Wilke CO. Large-scale analysis of post-translational modifications in E. coli under glucose-limiting conditions. Bmc Genomics. 18: 301. PMID 28412930 DOI: 10.1186/s12864-017-3676-8  0.56
2017 Deatherage DE, Kepner JL, Bennett AF, Lenski RE, Barrick JE. Specificity of genome evolution in experimental populations of Escherichia coli evolved at different temperatures. Proceedings of the National Academy of Sciences of the United States of America. PMID 28202733 DOI: 10.1073/pnas.1616132114  1
2016 Tenaillon O, Barrick JE, Ribeck N, Deatherage DE, Blanchard JL, Dasgupta A, Wu GC, Wielgoss S, Cruveiller S, Médigue C, Schneider D, Lenski RE. Tempo and mode of genome evolution in a 50,000-generation experiment. Nature. PMID 27479321 DOI: 10.1038/nature18959  1
2015 Quandt EM, Gollihar J, Blount ZD, Ellington AD, Georgiou G, Barrick JE. Fine-tuning citrate synthase flux potentiates and refines metabolic innovation in the Lenski evolution experiment. Elife. 4. PMID 26465114 DOI: 10.7554/eLife.09696  1
2015 Houser JR, Barnhart C, Boutz DR, Carroll SM, Dasgupta A, Michener JK, Needham BD, Papoulas O, Sridhara V, Sydykova DK, Marx CJ, Trent MS, Barrick JE, Marcotte EM, Wilke CO. Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation. Plos Computational Biology. 11: e1004400. PMID 26275208 DOI: 10.1371/journal.pcbi.1004400  0.56
2015 Maddamsetti R, Hatcher PJ, Cruveiller S, Médigue C, Barrick JE, Lenski RE. Synonymous Genetic Variation in Natural Isolates of Escherichia coli Does Not Predict Where Synonymous Substitutions Occur in a Long-Term Experiment. Molecular Biology and Evolution. 32: 2897-904. PMID 26199375 DOI: 10.1093/molbev/msv161  1
2015 Perry EB, Barrick JE, Bohannan BJ. The Molecular and Genetic Basis of Repeatable Coevolution between Escherichia coli and Bacteriophage T3 in a Laboratory Microcosm. Plos One. 10: e0130639. PMID 26114300 DOI: 10.1371/journal.pone.0130639  1
2015 Jack BR, Leonard SP, Mishler DM, Renda BA, Leon D, Suárez GA, Barrick JE. Predicting the genetic stability of engineered DNA sequences with the EFM Calculator. Acs Synthetic Biology. PMID 26096262 DOI: 10.1021/acssynbio.5b00068  1
2015 Maddamsetti R, Lenski RE, Barrick JE. Adaptation, Clonal Interference, and Frequency-Dependent Interactions in a Long-Term Evolution Experiment with Escherichia coli. Genetics. 200: 619-31. PMID 25911659 DOI: 10.1534/genetics.115.176677  1
2015 Graves JL, Tajkarimi M, Cunningham Q, Campbell A, Nonga H, Harrison SH, Barrick JE. Rapid evolution of silver nanoparticle resistance in Escherichia coli. Frontiers in Genetics. 6: 42. PMID 25741363 DOI: 10.3389/fgene.2015.00042  1
2015 Houser JR, Barnhart C, Boutz DR, Carroll SM, Dasgupta A, Michener JK, Needham BD, Papoulas O, Sridhara V, Sydykova DK, Marx CJ, Trent MS, Barrick JE, Marcotte EM, Wilke CO. Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation Plos Computational Biology. 11. DOI: 10.1371/journal.pcbi.1004400  1
2014 Deatherage DE, Traverse CC, Wolf LN, Barrick JE. Detecting rare structural variation in evolving microbial populations from new sequence junctions using breseq. Frontiers in Genetics. 5: 468. PMID 25653667 DOI: 10.3389/fgene.2014.00468  1
2014 Alnahhas RN, Slater B, Huang Y, Mortensen C, Monk JW, Okasheh Y, Howard MD, Gottel NR, Hammerling MJ, Barrick JE. The case for decoupling assembly and submission standards to maintain a more flexible registry of biological parts. Journal of Biological Engineering. 8: 28. PMID 25525459 DOI: 10.1186/1754-1611-8-28  1
2014 Sridhara V, Meyer AG, Rai P, Barrick JE, Ravikumar P, Segrè D, Wilke CO. Predicting growth conditions from internal metabolic fluxes in an in-silico model of E. coli. Plos One. 9: e114608. PMID 25502413 DOI: 10.1371/journal.pone.0114608  1
2014 Barrick JE, Colburn G, Deatherage DE, Traverse CC, Strand MD, Borges JJ, Knoester DB, Reba A, Meyer AG. Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq. Bmc Genomics. 15: 1039. PMID 25432719 DOI: 10.1186/1471-2164-15-1039  1
2014 Raeside C, Gaffé J, Deatherage DE, Tenaillon O, Briska AM, Ptashkin RN, Cruveiller S, Médigue C, Lenski RE, Barrick JE, Schneider D. Large chromosomal rearrangements during a long-term evolution experiment with Escherichia coli. Mbio. 5: e01377-14. PMID 25205090 DOI: 10.1128/mBio.01377-14  1
2014 Deatherage DE, Barrick JE. Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq. Methods in Molecular Biology (Clifton, N.J.). 1151: 165-88. PMID 24838886 DOI: 10.1007/978-1-4939-0554-6_12  1
2014 Renda BA, Hammerling MJ, Barrick JE. Engineering reduced evolutionary potential for synthetic biology. Molecular Biosystems. 10: 1668-78. PMID 24556867 DOI: 10.1039/c3mb70606k  1
2014 Hammerling MJ, Ellefson JW, Boutz DR, Marcotte EM, Ellington AD, Barrick JE. Bacteriophages use an expanded genetic code on evolutionary paths to higher fitness. Nature Chemical Biology. 10: 178-80. PMID 24487692 DOI: 10.1038/nchembio.1450  1
2014 Quandt EM, Deatherage DE, Ellington AD, Georgiou G, Barrick JE. Recursive genomewide recombination and sequencing reveals a key refinement step in the evolution of a metabolic innovation in Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America. 111: 2217-22. PMID 24379390 DOI: 10.1073/pnas.1314561111  1
2013 Barrick JE, Lenski RE. Genome dynamics during experimental evolution. Nature Reviews. Genetics. 14: 827-39. PMID 24166031 DOI: 10.1038/nrg3564  1
2013 Summers RM, Seffernick JL, Quandt EM, Yu CL, Barrick JE, Subramanian MV. Caffeine junkie: an unprecedented glutathione S-transferase-dependent oxygenase required for caffeine degradation by Pseudomonas putida CBB5. Journal of Bacteriology. 195: 3933-9. PMID 23813729 DOI: 10.1128/JB.00585-13  1
2013 Quandt EM, Hammerling MJ, Summers RM, Otoupal PB, Slater B, Alnahhas RN, Dasgupta A, Bachman JL, Subramanian MV, Barrick JE. Decaffeination and measurement of caffeine content by addicted Escherichia coli with a refactored N-demethylation operon from Pseudomonas putida CBB5. Acs Synthetic Biology. 2: 301-7. PMID 23654268 DOI: 10.1021/sb4000146  1
2013 Han P, Niestemski LR, Barrick JE, Deem MW. Physical model of the immune response of bacteria against bacteriophage through the adaptive CRISPR-Cas immune system. Physical Biology. 10: 025004. PMID 23492852 DOI: 10.1088/1478-3975/10/2/025004  1
2013 Wielgoss S, Barrick JE, Tenaillon O, Wiser MJ, Dittmar WJ, Cruveiller S, Chane-Woon-Ming B, Médigue C, Lenski RE, Schneider D. Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load. Proceedings of the National Academy of Sciences of the United States of America. 110: 222-7. PMID 23248287 DOI: 10.1073/pnas.1219574110  1
2012 Jerome JP, Klahn BD, Bell JA, Barrick JE, Brown CT, Mansfield LS. Draft genome sequences of two Campylobacter jejuni clinical isolates, NW and D2600. Journal of Bacteriology. 194: 5707-8. PMID 23012285 DOI: 10.1128/JB.01338-12  1
2012 Blount ZD, Barrick JE, Davidson CJ, Lenski RE. Genomic analysis of a key innovation in an experimental Escherichia coli population. Nature. 489: 513-8. PMID 22992527 DOI: 10.1038/nature11514  1
2012 Kholmanov IN, Stoller MD, Edgeworth J, Lee WH, Li H, Lee J, Barnhart C, Potts JR, Piner R, Akinwande D, Barrick JE, Ruoff RS. Nanostructured hybrid transparent conductive films with antibacterial properties. Acs Nano. 6: 5157-63. PMID 22519712 DOI: 10.1021/nn300852f  1
2012 Meyer JR, Dobias DT, Weitz JS, Barrick JE, Quick RT, Lenski RE. Repeatability and contingency in the evolution of a key innovation in phage lambda. Science (New York, N.Y.). 335: 428-32. PMID 22282803 DOI: 10.1126/science.1214449  1
2012 Reba A, Meyer AG, Barrick JE. Computational tests of a thermal cycling strategy to isolate more complex functional nucleic acid motifs from random sequence pools by in vitro selection Artificial Life 13: Proceedings of the 13th International Conference On the Simulation and Synthesis of Living Systems, Alife 2012. 473-480.  1
2012 Wolf LN, Barrick JE. Tracking winners and losers in E. coli evolution experiments Microbe. 7: 124-128.  1
2011 Wielgoss S, Barrick JE, Tenaillon O, Cruveiller S, Chane-Woon-Ming B, Médigue C, Lenski RE, Schneider D. Mutation Rate Inferred From Synonymous Substitutions in a Long-Term Evolution Experiment With Escherichia coli. G3 (Bethesda, Md.). 1: 183-186. PMID 22207905 DOI: 10.1534/g3.111.000406  1
2011 Nahku R, Peebo K, Valgepea K, Barrick JE, Adamberg K, Vilu R. Stock culture heterogeneity rather than new mutational variation complicates short-term cell physiology studies of Escherichia coli K-12 MG1655 in continuous culture. Microbiology (Reading, England). 157: 2604-10. PMID 21700661 DOI: 10.1099/mic.0.050658-0  1
2011 Woods RJ, Barrick JE, Cooper TF, Shrestha U, Kauth MR, Lenski RE. Second-order selection for evolvability in a large Escherichia coli population. Science (New York, N.Y.). 331: 1433-6. PMID 21415350 DOI: 10.1126/science.1198914  1
2011 Jerome JP, Bell JA, Plovanich-Jones AE, Barrick JE, Brown CT, Mansfield LS. Standing genetic variation in contingency loci drives the rapid adaptation of Campylobacter jejuni to a novel host. Plos One. 6: e16399. PMID 21283682 DOI: 10.1371/journal.pone.0016399  1
2010 Barrick JE, Kauth MR, Strelioff CC, Lenski RE. Escherichia coli rpoB mutants have increased evolvability in proportion to their fitness defects. Molecular Biology and Evolution. 27: 1338-47. PMID 20106907 DOI: 10.1093/molbev/msq024  1
2009 Barrick JE, Yu DS, Yoon SH, Jeong H, Oh TK, Schneider D, Lenski RE, Kim JF. Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature. 461: 1243-7. PMID 19838166 DOI: 10.1038/nature08480  1
2009 Barrick JE, Lenski RE. Genome-wide mutational diversity in an evolving population of Escherichia coli. Cold Spring Harbor Symposia On Quantitative Biology. 74: 119-29. PMID 19776167 DOI: 10.1101/sqb.2009.74.018  1
2009 Barrick JE. Predicting riboswitch regulation on a genomic scale. Methods in Molecular Biology (Clifton, N.J.). 540: 1-13. PMID 19381548 DOI: 10.1007/978-1-59745-558-9_1  1
2008 Weinberg Z, Regulski EE, Hammond MC, Barrick JE, Yao Z, Ruzzo WL, Breaker RR. The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches. Rna (New York, N.Y.). 14: 822-8. PMID 18369181 DOI: 10.1261/rna.988608  1
2008 Regulski EE, Moy RH, Weinberg Z, Barrick JE, Yao Z, Ruzzo WL, Breaker RR. A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism. Molecular Microbiology. 68: 918-32. PMID 18363797 DOI: 10.1111/j.1365-2958.2008.06208.x  1
2007 Barrick JE, Breaker RR. The distributions, mechanisms, and structures of metabolite-binding riboswitches. Genome Biology. 8: R239. PMID 17997835 DOI: 10.1186/gb-2007-8-11-r239  1
2007 Weinberg Z, Barrick JE, Yao Z, Roth A, Kim JN, Gore J, Wang JX, Lee ER, Block KF, Sudarsan N, Neph S, Tompa M, Ruzzo WL, Breaker RR. Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline. Nucleic Acids Research. 35: 4809-19. PMID 17621584 DOI: 10.1093/nar/gkm487  1
2007 Roth A, Winkler WC, Regulski EE, Lee BW, Lim J, Jona I, Barrick JE, Ritwik A, Kim JN, Welz R, Iwata-Reuyl D, Breaker RR. A riboswitch selective for the queuosine precursor preQ1 contains an unusually small aptamer domain. Nature Structural & Molecular Biology. 14: 308-17. PMID 17384645 DOI: 10.1038/nsmb1224  1
2007 Barrick JE, Breaker RR. The power of riboswitches. Scientific American. 296: 50-7. PMID 17186833  1
2007 Yao Z, Barrick J, Weinberg Z, Neph S, Breaker R, Tompa M, Ruzzo WL. A computational pipeline for high-throughput discovery of cis-regulatory noncoding RNA in prokaryotes Plos Computational Biology. 3: 1212-1223. DOI: 10.1371/journal.pcbi.0030126  1
2006 Lenski RE, Barrick JE, Ofria C. Balancing robustness and evolvability. Plos Biology. 4: e428. PMID 17238277 DOI: 10.1371/journal.pbio.0040428  1
2006 Puerta-Fernandez E, Barrick JE, Roth A, Breaker RR. Identification of a large noncoding RNA in extremophilic eubacteria. Proceedings of the National Academy of Sciences of the United States of America. 103: 19490-5. PMID 17164334 DOI: 10.1073/pnas.0607493103  1
2006 Sudarsan N, Hammond MC, Block KF, Welz R, Barrick JE, Roth A, Breaker RR. Tandem riboswitch architectures exhibit complex gene control functions. Science (New York, N.Y.). 314: 300-4. PMID 17038623 DOI: 10.1126/science.1130716  1
2005 Corbino KA, Barrick JE, Lim J, Welz R, Tucker BJ, Puskarz I, Mandal M, Rudnick ND, Breaker RR. Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria. Genome Biology. 6: R70. PMID 16086852 DOI: 10.1186/gb-2005-6-8-r70  1
2005 Barrick JE, Sudarsan N, Weinberg Z, Ruzzo WL, Breaker RR. 6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter. Rna (New York, N.Y.). 11: 774-84. PMID 15811922 DOI: 10.1261/rna.7286705  1
2004 Mandal M, Lee M, Barrick JE, Weinberg Z, Emilsson GM, Ruzzo WL, Breaker RR. A glycine-dependent riboswitch that uses cooperative binding to control gene expression. Science (New York, N.Y.). 306: 275-9. PMID 15472076 DOI: 10.1126/science.1100829  1
2004 Barrick JE, Corbino KA, Winkler WC, Nahvi A, Mandal M, Collins J, Lee M, Roth A, Sudarsan N, Jona I, Wickiser JK, Breaker RR. New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. Proceedings of the National Academy of Sciences of the United States of America. 101: 6421-6. PMID 15096624 DOI: 10.1073/pnas.0308014101  1
2004 Nahvi A, Barrick JE, Breaker RR. Coenzyme B12 riboswitches are widespread genetic control elements in prokaryotes. Nucleic Acids Research. 32: 143-50. PMID 14704351 DOI: 10.1093/nar/gkh167  1
2003 Barrick JE, Roberts RW. Achieving specificity in selected and wild-type N peptide-RNA complexes: the importance of discrimination against noncognate RNA targets. Biochemistry. 42: 12998-3007. PMID 14596615 DOI: 10.1021/bi035163p  1
2003 Winkler WC, Nahvi A, Sudarsan N, Barrick JE, Breaker RR. An mRNA structure that controls gene expression by binding S-adenosylmethionine. Nature Structural Biology. 10: 701-7. PMID 12910260 DOI: 10.1038/nsb967  1
2003 Mandal M, Boese B, Barrick JE, Winkler WC, Breaker RR. Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria. Cell. 113: 577-86. PMID 12787499 DOI: 10.1016/S0092-8674(03)00391-X  1
2003 Sudarsan N, Barrick JE, Breaker RR. Metabolite-binding RNA domains are present in the genes of eukaryotes. Rna (New York, N.Y.). 9: 644-7. PMID 12756322 DOI: 10.1261/rna.5090103  1
2002 Barrick JE, Roberts RW. Sequence analysis of an artificial family of RNA-binding peptides. Protein Science : a Publication of the Protein Society. 11: 2688-96. PMID 12381850 DOI: 10.1110/ps.0208902  1
2001 Barrick JE, Takahashi TT, Ren J, Xia T, Roberts RW. Large libraries reveal diverse solutions to an RNA recognition problem. Proceedings of the National Academy of Sciences of the United States of America. 98: 12374-8. PMID 11675487 DOI: 10.1073/pnas.221467798  1
2001 Barrick JE, Takahashi TT, Balakin A, Roberts RW. Selection of RNA-binding peptides using mRNA-peptide fusions. Methods (San Diego, Calif.). 23: 287-93. PMID 11243841 DOI: 10.1006/meth.2000.1139  1
2000 Liu R, Barrick JE, Szostak JW, Roberts RW. Optimized synthesis of RNA-protein fusions for in vitro protein selection. Methods in Enzymology. 318: 268-93. PMID 10889994  1
1986 Amsden TW, Barrick JE. Late Ordovician-Early Silurian strata in the Central United States and the Hirnantian Stage. Bulletin - Oklahoma Geological Survey. 139.  0.01
1980 Amsden TW, Toomey DF, Barrick JE. Paleoenvironment of Fitzhugh Member of Clarita Formation (Silurian, Wenlockian) southern Oklahoma. Oklahoma Geological Survey, Circular. 83.  0.01
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